Beamed Up
by Zoja
Summary: "Colonel… We lost Doctor Weir on the replicator planet. Can you lock on her locator beacon and beam her up?" What if Carter managed to get Elizabeth to the Apollo before the replicators made it impossible?
1. Chapter 1

**A/N:** It's the first story I've written in a few years so I'm the first to admit I'm a bit rusty. After some debate I eventually decided to post it; I wasn't sure I should at first as there is a part of me that considers turning it into a longer story one day, but who knows when - or even if - it's going to happen, and this part can just as well stand as a one-shot, so why not just release it. And if I ever do write more for it, I'll just turn it into a multi-chapter story. No beta reader means that the entire proof-reading was done by me, so I apologize for all the mistakes. Enjoy.

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"Colonel… We lost Doctor Weir on the replicator planet. Can you lock on her locator beacon and beam her up?"

John's heart was pounding in his chest as he waited for the answer. He knew the chance was small; the device was probably the first thing that the replicator would want to get rid of to make sure Elizabeth couldn't escape that way, knowing that they possessed this kind of technology. It hadn't exactly been long since that last moment they saw her before making a run for the jumper, but it had taken them a few moments and it was certainly more than enough time for the replicators to get busy with their newly captured prisoner, something he didn't even want to think of.

Even though it was only a couple of seconds before the woman spoke up, to John it felt like a lifetime. He could still see Elizabeth's face, her voice was ringing in his ears; it mixed with his own, screaming at him how he should never have just left her there. He thought watching her unconscious in the infirmary, hooked up to all the machines, knowing that she would most probably never wake up, was horrible but in that moment, he felt even worse. This time, what happened to her was his fault; he was the one that just ran away, leaving her surrounded by the enemy.

"Done" replied Carter, and that one, simple word made John feel as if a huge weight was lifted off his chest. It wasn't, however, something he had too much time to think about; even through the open communications channel he could hear Elizabeth's angry voice, screaming how they shouldn't have done that.

He wasn't even listening, focused on getting to the ship as quickly as possible. Still, he knew that in a way, she was right; beaming her up from that planet with her connection to the replicators still active was a very risky move, but he had no doubts McKay would be able to figure something out, especially with Colonel Carter and Doctor Lee present on the Apollo and available to help him. There had to be a way and if there was anyone that could find it, these three were among the most likely people to do it.

"Where is she?" was the first thing he said when he landed the jumper in the F-302 bay.

"A prison cell" came Carter's hesitant answer. Her voice left no doubts she expected that John wouldn't be happy about it. "She insisted we should lock her up, preferably someplace with a jamming system."

_Of course she did_, thought John as he headed to that section of the ship. It was difficult to argue that it was probably the best course of action, too; assuming that not only were they able to know her exact location, but to see and hear everything that she could, having her stay someplace where she wasn't aware of anything that was going on the ship was their best option. Just because she was taken there didn't mean that her anger was alleviated; if anything, it only seemed to increase the second her eyes fell on John.

"Have you completely lost your mind?!" she shouted.

It was just the beginning of a very long rant. No matter how calm and stoic she always tried to remain regardless of the situation, there were times when even she reached her breaking point and John was one of those people that had been able to witness it; he had even found himself at the receiving end of her anger a few times. Even so, he had never seen her that furious; just one glance at her enabled anyone to see she was fuming and he couldn't help feeling that he should be grateful for the force field separating the two of them, for he would, at the very least, be getting quite a fierce slap to the face if it wasn't.

Of course, he was getting blamed for the entire situation. It was clear that in her mind, he was responsible for the fact that she found herself on the Apollo despite having been left on the replicator homeworld, and he wasn't even going to argue with her. Sure, he could tell her the crew of the ship would try to locate her on the planet the moment they realized she was missing even if he didn't make that request, simply because it was the right thing to do, but the truth was, he couldn't be sure. She was compromised, after all; the nanites in her body, her link to the replicators posed a very serious threat to the Apollo as well as Atlantis, possibly even Earth, so he just couldn't with all honesty say that they wouldn't decide that leaving her behind was the best course of action.

He might have been fully prepared for it but the longer she went on, the more his resolve to keep his composure weakened. He intended to wait her out, to just let her get it all out before attempting to talk to her, but there came a point when he just couldn't take it anymore.

"It was the stupidest, most irresponsible…"

"So we were supposed to just leave?!" he shouted, interrupting her. "Get the jumper to the Apollo and simply leave you there, at the mercy of the replicators?!"

"YES" she stated exasperated, as if it was the most obvious thing in the world.

"Do you have any idea what they would do to you?!"

"Do you have any idea what _I_ can do to you, to everyone?!" she immediately countered, looking around in disbelief.

She was clearly searching for support from anyone else present in the room, but they were just standing there quietly, watching the exchange. Those that worked with the two of them on Atlantis knew better than to get in the middle of one of their arguments; not only would it result in finding themselves at the receiving end of both John and Elizabeth's anger, but they also knew that these two were always able to work it out between each other in the end. The others had a feeling it was better to stay out of it, too; it didn't seem like there was anything that could be said to change either of their minds.

"We won't let you" said John, emphasizing every word. "Colonel Carter and Doctor Lee are already working on jamming any communication between your nanites and the replicators, and with McKay now here too, I'm sure they'll figure it out in no time."

"And what if they won't?!" she paused, wanting to scream in frustration that he wasn't seeing her point. "What if they won't figure it out and the replicators come straight after us to Atlantis, which we have no possible way of defending against them?! I will not be the reason for the death of everyone in the city!"

"We WILL NOT let that happen" shouted John, as frustrated as she was. "You're here, you're coming with us to Atlantis; end of topic. And if you really thought I was just going to leave you there, so they can do whatever they want to you – which I have no doubts would not be pleasant things – then you are the one, who has lost her mind. I told you on day one, we do not leave our people in the hands of the enemy and this has not changed."

Elizabeth opened her mouth, to counter his words yet again but she eventually decided against it. It was obvious she was getting nowhere, something that honestly shouldn't come as a surprise considering she was dealing with John Sheppard, but now that she had a chance to vent majority of her anger, she was fully able to admit that this argument was actually pointless. There was nothing she could do to change what happened, just like there was nothing she could do to change the situation she was now in, which she was the first person to admit was actually a good thing. All she really could do was hope John was right.

As it later turned out, he was – or at the very least it seemed that way. The three scientists took a while but it seemed that they did, in fact, manage to figure something out, even if they claimed it was only a temporary solution, but something that could buy them at least enough time to help Atlantis. John insisted to stay with her the entire time, claiming it was for the sake of security but nobody really bought that explanation, but he was eventually forced to leave when they reached the city. She had no idea just how much time had passed since then; as much as she wanted to, she couldn't go with him for fear of revealing their location to the replicators, and it felt like it lasted eternity before she saw someone other than the two officers that were assigned to keep an eye on her.

Much to her surprise, the person that came to inform her about the success of the plan turned out to be Samantha Carter. She was one of the last people she expected; she thought it would be John, maybe Rodney, really anyone from the expedition, but not the Colonel. They might have not exactly disliked each other, but there was no love lost between them either; other than Elizabeth's very brief time as the commander of Stargate Command, they didn't even have all that many opportunities to interact with each other, and to say that they simply respected each other was probably best way to describe their relationship. She definitely didn't feel like they were close enough for the Colonel to want to make sure she was appraised of the situation.

"I figured you'd probably like to know that everything worked out" she said as if she was reading her mind. "Atlantis has safely landed on a new planet and is once again connected to the intergalactic bridge. Don't worry, we chose an entirely new location just in case they probed your mind for this information" she explained quickly, before Elizabeth could voice her worries. "It doesn't look like the replicators are aware of where we are."

"Good," Elizabeth sighed with relief. It was what she was probably most afraid of, that despite all their attempts to avoid it, the replicators would somehow manage to find them. "What about the bad news?"

Carter had to suppress the urge to smile at the question; of course, everything they race came upon ever since they began to use the stargate rarely finished with 'it worked out' that wouldn't come with any but and the Doctor had no reason to think this situation was any different.

"We're having problems finding a quick and permanent solution for your situation. We all agree that keeping you locked up like this for an indefinite period of time is not a good solution, and creating a small jamming device that you could carry on yourself at such a short notice is basically impossible. Not to mention, there's no guarantee the replicators wouldn't eventually figure out how to get around it" she explained with a sympathetic smile. "We obviously can't deactivate your nanites as they are what is keeping you alive and I don't imagine the replicators will allow us to simply disconnect you from the network" she continued and as much as Elizabeth appreciated the explanation, she was beginning to grow tired of the suspense that the other woman was keeping her in. "We could theoretically try and reprogram your nanites so that they basically serve as nothing more than replacement for the damaged cells but…"

"As long as the replicators are out there, there will never be full certainty that my nanites won't one day be used against us by them" finished Elizabeth. "What's going to happen to me, then?"

"We've agreed you that the best thing to do will be to put you into stasis until we actually can come up with something permanent. That way you won't pose a threat while we get more time to find a solution."

Elizabeth remained silent as she pondered on what she had just heard. Back on the replicator planet, she was actually prepared to die; at that time, it seemed like the only way to enable John, Ronon and Rodney to escape and if giving her life meant that she could save her people and Atlantis, she was more than willing to do it. The bright light that brought her to the Apollo was a surprise, and even though she still wasn't convinced it was a wise decision, she allowed herself to hope that maybe it wasn't all over for her, yet. Now, she wasn't so sure; putting her into stasis to buy more time made sense, but how long would it take them to find an actual solution? Especially, that it was going to be a side project, probably assigned to one person and she had a feeling Rodney would insist for it to be him. That meant he would only work on it in his free time, when he wasn't on a mission or trying to save the city or the galaxy.

"It really is…" began Sam, seeming to mistake her silence for lack of confidence or approval.

"I understand. So, I guess they're preparing the stasis pod as we speak?"

"They are. John was quite insistent Rodney should make sure there would be no problems with it." A hint of smile appeared on Carter's face as she thought of it. "He's really protective of you."

"It's kind of in his job description" Elizabeth chuckled, remembering the conversation the two of them once had, when he said the exact same thing to her. "Not sure if you know, when we first came to Atlantis and Colonel Sumner was the military commander, John was only supposed to operate Ancient technology and, if need be, serve as my personal bodyguard."

Of course, Sam was aware of that. She heard of the heated argument Elizabeth had with Sumner after she invited John to join the expedition, something that the Colonel was strongly opposed to. In the end, they reached an agreement that since Sheppard wasn't going with them because he was military, but because of his seemingly innate talent to operate Ancient technology, he was going to be assigned to her and answering directly to her. Yet, Sam – just like anyone else – couldn't help wondering just what happened during that first year that when they established contact with Earth, Elizabeth didn't want to hear about John being replaced. It made a lot of people wonder just how close the two of them had become, gave rise to many rumours but so far, they all remained unconfirmed. Still, John's behaviour ever since they rescued the four of them from the replicator's planet really made her see why so many people believed there had to be more between these two.

"Could I talk to him before I'm taken to Atlantis?"

"Sure" smiled Carter.

He arrived before long, a little surprised by the request but if she wanted to talk to him, it was better to do it before they beamed her down to Atlantis. It would be race against time, hoping the command they activated would keep the replicators so occupied they weren't going to pay any mind to Elizabeth or her location during the short time between her arriving in the city and entering the stasis pod.

"I'm sorry we don't have a better solution" he said, looking at her somberly. He couldn't say he was happy with it but there was no other option and he was forced to accept it. "Look, we'll figure something out. I'll stand over Rodney with my gun, threaten to shoot him if I have to, but we'll come up with something."

"I know" she gave him a weak smile. "If there's anyone I trust to get me out of this mess, it's you and Rodney. But, in case it doesn't work, I need a favour from you."

"Elizabeth…" he began, having a feeling where this was going but she didn't let him say anything more.

"John, listen to me. I know you will do your best but you have no way of knowing if Rodney or anyone else for that matter will be able to figure _anything_ out or how long it's going to take. It may take a month, a year or it may not even happen within your lifetime if ever. I don't want to be woken up only to find out that everyone I cared about is dead going to be not too long from then."

"You can't seriously be asking me for _that_" he hissed, a mix of anger and disbelief showing up in his features.

"You're the only one I can trust to respect my wishes enough to do that, you owe me that much."

She honestly hated to pull that on him; it wasn't a lie, there was no other person in Atlantis or even the entire Stargate program that she trusted more than John, and she knew he was the only one that would do what she wanted, no matter the cost. He had already proven that by refusing to let Rodney activate her nanites to save her life and even though McKay eventually went behind his back and did it anyway, it wasn't something she could hold against John. She knew that his silence was an expression of strong disapproval, but seeing that he didn't try to counter her in any way, she continued.

"If it comes down to a situation like this, when it's been decades and there's no solution or if you have to abandon the city or anything else that would mean I've lost you all, I want you to use the kill switch on my nanites. You need to understand, I don't want to spend eternity in stasis or wake up to a society that will be completely foreign to me and know that I'll never see any of you again."

Before he managed to say anything, Colonel Carter once again went into the room with an apologetic expression on her face. Apparently, everyone was wondering what was taking so long since Atlantis was ready for Elizabeth to be beamed into the city already a while ago. Soon, all three of them were once again standing in Atlantis and Elizabeth let out a heavy sigh as she stood facing the stasis pod.

"John, promise me you'll do it" she said as she stepped into the stasis pod and turned around, looking directly at him.

He was silent for a moment, her request weighing heavily on his heart. He couldn't deny that he understood why she wanted him to do it, but it still felt like a horribly unfair request. She was basically asking him to kill her, how could she expect him to just accept it without complaints when even thinking he had lost her, twice, left him feeling more terrible than anything else in his life? She was right, though; he respected her too much to against what she wanted.

"I promise."

She sent him a small, thankful smile and nodded to Rodney.

"We will get you out of there, Elizabeth, I swear" spoke McKay before he pressed a few buttons on his tablet and the pod activated with a soft hiss.

Elizabeth managed to get a last look around the room, at the people that gathered in it and closed her eyes. She thought of the expedition, of the people that became her friends over the past three years, of the city she grew to love so much. It was the last thought she had before her consciousness slipped away and everything faded to black.


	2. Chapter 2

**A/N:** It took me much longer than I thought it would, but here is the first part of the continuation that I assured a few people I am working on. I'll try my best to update regularly. In the meantime, I apologize for all the mistakes and I hope you won't be disappointed. Enjoy!

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_Six months later_

Sam sighed heavily, leaning forward and hiding her face in her hands as she finished reading the proposal submitted to her by John and Rodney.

She had been expecting something like this ever since they destroyed the replicators. In fact, she was surprised that they didn't come to her office the second they were all back in Atlantis, and the only reason she could think of for why was that they wanted to make sure that their plan was as close to flawless as possible. She was actually curious about what they were going to come up with as, from her point of view, there just didn't seem to be any truly satisfying solution, which was also why she had been dreading this moment so badly.

She had to admit that they had really thought it through. It was clear that they acknowledged the fact that the active nanites would always be a potential threat and did their best to minimize the risk. The number of safety precautions that Rodney had put into the programming was reaching truly paranoid levels, but it was the incorporation of the kill switch that really took her by surprise. It made her admire their resolve as she couldn't imagine either of them being comfortable with it, even though she knew that they were right with their comment of _'if she could speak for herself, she would ask for a way to ensure that she can't cause any harm if the nanites were trying to take over'_. She might not have known Elizabeth Weir too well, but Sam had seen the way she acted when she was beamed onto the Apollo; she could also see how much the woman loved this place and how dedicated she was to this expedition every single day.

It made her realize just how difficult her position really was, too. She might have received a pretty warm welcome when she arrived in Atlantis, despite being an outsider who came to replace the leader, who had earned their trust and loyalty, but she knew that they accepted her only because they didn't really have another choice and under these particular circumstances, they could hardly blame anyone for the change in leadership. Still, if it came down to choosing between her and Weir, she was sure that many – if not large majority – of these people would choose Weir and by rejecting this proposal, not only would she undermine her own standing with them, but she could actually find herself facing mutiny when John and Rodney were to attempt to help Weir anyway.

And she had no doubts that these two would do something, regardless of her answer, just like she knew that between John and Rodney's familiarity with the city and its systems, and the support the two would receive from the other people in Atlantis – be it by openly refusing to stop them or indirectly, by not really trying – she didn't stand a chance in stopping them. She wasn't even sure that she wanted to, either, especially that if the roles were reversed, she wouldn't even hesitate. She had already proven that, having been willing to put everything on the line to help Jack, and it was a really crazy case of karma that she now found herself facing a similar decision about the very same woman, whom she had practically blackmailed to help her back then and who had actually given in.

On the other hand, as long as the plan involved leaving the nanites active, she simply couldn't imagine the IOA going along with it. Minimizing the threat wouldn't be enough for them; they would want absolute certainty and it wasn't something they could give them without deactivate the nanites, which they couldn't do. She knew that Rodney initially hoped to program the nanites in such a way that they would actually create organic material to fix the damaged parts of Elizabeth's brain, which would have been perfect, but now that it had already been repaired with the use of nanites, all tests indicated that this option was, unfortunately, out of the window. This meant that Elizabeth Weir would most likely depend on the nanites for the rest of her life and, as a result, would always be seen as too big of a security risk to be woken up.

A few moments later, Sam found herself walking through the corridors of Atlantis, heading towards the stasis chamber room. Over the past few months, it had become natural for anyone on Atlantis to assume that whenever they couldn't find John Sheppard anywhere, he was most likely 'visiting Elizabeth' and it was exactly where she found him. He was standing in front of the stasis chamber, looking at the woman in front of him and talking about what was happening in Atlantis, almost as if he was trying to keep her up to date on everything, despite being aware that she couldn't hear him.

"I figured I'll find you here" she spoke, alerting him to her presence as she walked further into the room and stopped at his side.

"Let me guess" he replied, never taking his eyes off of Elizabeth. "You're not going to let us wake her up."

"Actually, I was going to ask what you and Rodney plan to do about the IOA" she said. "You must realize that they'll never approve of your plan."

"Not unless we leave them no choice in the matter" he remarked, raising Sam's curiosity. "If we can get you on our side, we'll also have General O'Neill and even the IOA recognize his authority."

"And if you can't?" she asked, slightly surprised by John's assumption but at the same time, she had to admit that he probably had a point; while they didn't always see eye to eye about everything, Jack O'Neill was always willing to trust her and she had no idea what she would have to do for him to be against it.

"I would say that we could take Atlantis and declare independence, but I don't think we have enough power for that" he mused. "A little sabotage of access to Atlantis' systems and taking something smaller, like – theoretically speaking – a jumper or two, is another matter."

"So, you're saying that you're going to do it regardless of the answer and it's just a matter of whether or not you're going to wreak havoc?"

"I would never say that" he said, but the hint of defiance in his voice left no doubts that it was exactly what he was implying.

Sam had to smile, once again brought back to what was probably her most memorable conversation with Elizabeth Weir when she realized that he used the very same words as she did back then. The similarities truly were quite striking and as she watched John, she understood that they ran even deeper than that.

As someone, who had actually found herself as the object of the rumour mill, she was the last person to believe the rumours but she also knew that they usually weren't born out of nothing and she was starting to realize that the little comment she overheard about John and Elizabeth being the Atlantis counterparts of her and Jack might not have been as ridiculous as she had initially believed it to be. It was difficult not to see the change that had occurred in John or how determined he was to fight on Elizabeth's behalf and now, Sam could also see how far he was willing to go and all that affirmed her in her belief that he actually cared about Elizabeth much more than he was letting on.

"I do realize what we're asking you to do and the position it will put you in but Elizabeth deserves better than this" he spoke again, breaking the silence that fell between them as he motioned towards the stasis pod. "If the IOA refuse to see reason, Rodney and I are willing to take full blame for everything. We'll happily make it look like you didn't know about anything and we didn't really leave you any choice. They won't be able to prove otherwise."

Sam nodded in acknowledgement, understanding that they really had thought about everything, including the potential repercussions of their action that the rest of the expedition would have to face. It also suddenly dawned on her that they weren't trying to force her hand as much as they were willing to put trust in her, offering her a chance to show what kind of a commander she wanted to be. They could easily have gone behind her back but chose to include her, to give her an opportunity to prove that she cared about her people, to earn their trust and loyalty and, as a result, also that of the Atlantis expedition, and the fact that they were willing to do that meant more to her than anything.

It was the kind of commander she had always wanted to be, after all. Someone, whom the people would be willing to follow because they believed her to do the right thing rather than because they had no other choice. It might not be the type of situation that she would choose to start building this kind of reputation, but it was the decision that she was facing and she knew that one way or another, it was something that would probably follow her for the rest of her career. She had, of course, known that making difficult choices was a natural part of being in charge but now, that she was in that very position herself, she found herself even more full of respect to all of those, whom she had known to be able to do the right thing.

"Very well" said Sam. "Talk to Rodney, make him check everything one more time, just to be sure."

The change in John, when he finally allowed himself to hope that everything could actually turn out well, was practically instantaneous. Until now, he just didn't dare to hope that it could end in any other way than with the break out, which would force them to live as refugees for the rest of their lives. He might have been willing to pay this price, but it didn't mean that it was something he was looking forward to if he could avoid it.

"Yes, Ma'am" he replied with a smile, which reflected a mix of such an untamed relief and happiness that she didn't even want to imagine what his reaction would be if she was to give him a different answer, no matter how terribly she would feel about it. "And thank you."

"You'll thank me when everything turns out well" she said, offering a smile of her own before her gaze moved to Elizabeth, completely oblivious to the conversation that was taking place right in front of her. "She'll be happy to know that she has friends, who are willing to become fugitives from her own planet to help her."

"Happy?" John snorted. "She'll want to strangle McKay and me, without any influence from the nanites. Still, if my actions give her a chance of getting her life back, I'll happily face her wrath."

"You really care about her, don't you?" asked Sam, smiling when he looked at her and the expression on his face, full of uncertainty about what he should say not to incriminate himself, gave her all the confirmation she was looking for.

"She took a risk and offered me a second chance despite everyone telling her not to" he said. "She brought me here, she made me the military commander, she fought to let me keep the position and even got me a promotion. I owe her, well, everything."

"Right" she hummed, not really trying to hide that she didn't believe it was only that, even if she recognized that he had a point.

"Well, you of all people know what it's like to, you know" he muttered, hiding his hands in his pockets.

"Care about someone a lot more than you're supposed to?" she offered, smiling at the memory. "Yeah, I do."

"With you in charge, it's not more than I'm supposed to anymore, is it?"

"No, I suppose not" she agreed.

With that, Sam turned to leave, giving John the opportunity to go back to his one-sided conversation in private. She had a very important, intergalactic email to write and she wished she could see the look on Jack's face when he would read it, as she could already hear his irritated 'Carter!' in her mind that she would hear in person the next time she would see him.

John, in turn, waited for when she was out of earshot to step closer to stasis chamber and place his hand on the transparent barrier that separated him from Elizabeth.

"See, Lizbeth? I told you Carter was okay" he spoke, completely undeterred by the fact that she didn't even so much as twitch. "So hang in there, just a little longer."


	3. Chapter 3

**A/N:** Thank you very much for your response, follows and faves and especially reviews. It makes me super motivated to see that there are still people out there, who are interested in John/Elizabeth stories. My plan, generally, is to try to update this story on Mondays but, seeing how I have to upload chapter 4 on Thursday, as I'm not going to have access to my laptop next Monday and I don't really like using my mobile for anything fanfic-related other than reading, I chose to publish this one a little early as well. As always, I apologize for any mistakes and hope you're going to like it.

* * *

Preparations began almost immediately and the news that they were going to revive Elizabeth Weir spread through Atlantis like wildfire. Just like Sam predicted, it quickly became a matter, which united the entire personnel. No matter what kind of opinion someone had about the first leader of Atlantis, they all agreed that spending one's entire life in stasis, not dead but not quite living either, was not something they would wish on anyone.

As he stood by the windows overlooking the isolation room, watching Keller perform all kinds of test, John couldn't help thinking that they were going a little too far. He was all for safety and he knew that they needed to take measures to prove to the IOA that Elizabeth really wasn't a threat or security risk, but some of the precautions seemed more appropriate for someone, who was a carrier of a deadly virus or turning into a wild, uncontrolled beast – or even a bug, rather than presenting a risk of transmitting sensitive intel to the enemy.

Only the awareness that the more careful they were, the higher their chances of convincing the IOA to leave her be would get that prevented John from speaking up, as well as the knowledge that Elizabeth wouldn't accept anything less. He knew that in a way, she could actually be more difficult to persuade than anyone else. She might have been willing to give almost everyone the benefit of the doubt, except for herself, and the very first thing she told them, when she regained consciousness, was that they never should have even thought about reviving her if they couldn't deactivate her nanites.

"How is she?" asked Sam as she stopped next to John.

"Much calmer than I expected" he replied and, almost as if on cue, Elizabeth lifted her head and looked straight at him. Even though she did that to avoid looking at Keller, when the doctor was preparing to cut her hand in order to check if the nanites would repair the damage, her gaze was still full of reproach and sending a very clear message that they were going to have a very serious conversation.

"Making the incision, now" sounded Jennifer's slightly distorted voice as she provided commentary for the recording that they were making to have a proof of the results.

They watched as Keller made a careful cut on Elizabeth's hand, which immediately began to bleed. The doctor waited for a minute, which they had determined was more than sufficient time for the nanites to react, allowing the recording to capture that nothing was happening before she started treating it.

"Everything looks good so far" continued John. "According to all tests Keller and McKay have come up with, the nanites don't do anything more than serve as a substitute for the damaged cells, just like Rodney said they would."

"Good" murmured Sam.

Elizabeth, however, wasn't convinced and looked extremely uncomfortable, even after they finished all the tests and left her alone. When John entered the room some time later, he wasn't sure if he felt more relieved or more worried by the fact that she didn't jump at the chance to chew his head off, which he expected to be the first thing she would do as soon as she saw him. He knew she was aware of his presence, having noticed how she stiffened up when he entered, but was apparently choosing to ignore him and he wondered if she was doing it because she knew that in his opinion, finding himself on the receiving end of her silence when she was angry was much more terrifying – and guilt inducing – than any scolding she could give him.

"Thought you might be hungry" he said, putting the tray he brought on the table. He had tried to turn it into a peace offering of sorts, deliberately choosing all of her favourites in hopes of placating her, but he would lie if he claimed that he was surprised she ignored it as well. "Even if you're not, you do have to eat something."

She still didn't say anything and refused to look at him, and if he didn't know her as well as he did, he would have missed the way she pressed her lips more tightly together and clenched her jaw that gave away the fact that she wasn't quite as indifferent and emotionless as she would have liked him to believe. As it was, it made him realize that she was fighting an internal battle, trying to decide whether she was so angry that she didn't even want to talk to him or actually wanted to take it out on him.

Not wanting to push too far, but trying to make her realize that he wasn't going to give up that easily, he moved to sit down in one of the chairs that they had brought, when trying to make the room a little less sterile for the duration of the observation period, during which she was prohibited from leaving and constantly monitored for any irregularities. He wasn't sure what else he could do with the cameras recording everything that was happening in the room, uncomfortable with the idea of a personal conversation that would be available for everyone to watch and listen to.

Luckily, she either understood his message or decided to show him mercy – perhaps a combination of both – and turned her head to look at him.

"You shouldn't have done it" she finally said, sighing heavily, and – much to John's surprise – all he could hear in her voice was resignation.

"It was the right thing to do" he replied, with a little more force than he intended. "With the replicators gone, there is no reason for you to stay in stasis anymore."

"The collective still exists" she insisted. "My nanites are more than enough for them to rebuild themselves, all they need to do is find a way to overcome Rodney's programming…"

"That's what the damn kill switch is for!" he interrupted and raised his eyebrows in confusion at the surprised expression that appeared on her face. "Right, I forgot McKay didn't tell you" he murmured, as he realized that with the entire focus being on conducting all those tests, the scientist limited his explanation to the necessary basics, intending to return to the details later. "I forced him to write the kill switch into the code. If they ever try to overcome the programming and take over, the kill switch will activate and shut them down."

"And what if it doesn't?"

"Then we'll activate it manually" spoke John, huffing in frustration at her stubborn pessimism. "I thought you trusted me."

"I do but…" she began, but he didn't let her finish.

"Then trust me with this, too. I would never have done this if I didn't believe it was going to be alright" he said, knowing she would understand what he was really trying to say. _I would never have done this to you._

Elizabeth sighed, lowering her gaze to the floor. She really wanted to believe that. One of her first things when she regained consciousness, remembered what had happened and realized that they had taken her out of stasis was that John would never have agreed to take a risk like that, that he would never allow anyone to put her in this kind of situation again. When she saw him, though, watching everything from the observation deck, she understood, that he had actually played a part in it this time.

Knowing that, her first guess was that they needed her to execute some kind of a plan against the replicators – it was the only sensible reason she could think of for them to take the risk of reviving her. Her nanites were a double-edged sword, after all; they could put them at danger from the replicators, but they could also give the team an advantage over them, just like during the mission to steal a ZPM, and she would be willing to do anything that was necessary to help.

Then, Rodney explained that it wasn't the case at all and all she could think about was how it was a very bad idea. Most of all, however, she was scared. As much as she trusted her friends, as much as she wanted to believe in them, she knew from experience that their ideas hardly ever went exactly according to plan and in this case, any kind of complications could be extremely bad for all of them.

First, there was the possibility that despite all the security measures Rodney put in the programming to prevent it from happening, the nanites would still find a way to take over. She was grateful for the kill switch, it made her feel a little better, but she couldn't help wondering if there was a way for the nanites to somehow disable it, without triggering its activation, before they were to do anything else. If it was John's idea, he probably insisted that it should be triggered by any suspicious activity from the nanites so the logical answer should be no, but she just couldn't be certain.

Potential repercussions of the nanites taking over was yet another thing she didn't even want to think about. She didn't want to die, but it wasn't even the kill switch that she was the most afraid of. From what she understood, it was supposed to be instant – she would simply get knocked out immediately, dead in that very same moment. It was the effect it would have on the others that actually worried her, and not only the fact that quite a few of them could lose their jobs over it. She had no doubts that it would also make them feel guilty, especially John and Rodney, and she didn't want to cause her friends any more problems or anguish.

There was also the IOA of course. From what she understood, the organization didn't exactly give them the green light to act, but with the constant recording, she didn't dare to ask about the details of how they intended to take care of this particular problem. They must have had some kind of a plan, especially that it was pretty obvious that the IOA weren't going to be happy about her revival and the potential risk it presented, no matter how infallible the security measures would be. With everything else that they took into consideration, she couldn't imagine that John and Rodney didn't come up with some kind of countermeasures for the IOA's action as well.

If she was to guess, they probably intended to flee – it was the most logical option. She was actually surprised that they hadn't done it even before she woke up, instead choosing to put their trust into the people and, as much as she wanted to believe the best of everyone in Atlantis, they could never be fully certain what someone's real feelings and opinions were. Yet, despite knowing that they could easily survive on their own – even more so if they were to receive help from their allies – she wasn't too fond of the idea of spending the rest of her life on the run, and she hated to think what it would do to her mother.

Ultimately, however, she had to admit that there wasn't really anything she could do about any of the problems. She was completely at the mercy of others and she didn't like it. She understood it, yes, but absolutely hated this feeling of helplessness and uncertainty. She didn't have any other choice, though; she had to comply with everything, as any sign of protest from her could be read as suspicious and end up causing more harm than good. All she could do was believe in her friends, and if there was any person that she had unwavering faith in, it was John.

"Okay" she finally said, raising her head to meet his gaze once again. Overthinking wouldn't do her any good, she needed to believe that it was going to be fine. "I'll trust you."


	4. Chapter 4

**A/N:** I publish this chapter today, just like I promised. The next one, on the other hand, may be a little delayed, but I'll do my best to publish it on the 27th. I know it's a long wait but, considering that it'll be full of sparkiness, it should be worth the wait :) Anyway, as always I apologize for the mistakes and hope you'll enjoy!

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John knew that getting Elizabeth to agree not to think negatively was only the tip of the iceberg, that it would take much longer for her to truly come around and truly believe that it was going to be okay. Still, he was happy to see that she was actually making an effort instead of dwelling on everything that could potentially go wrong, slowly going back to being the Elizabeth he knew instead of a gloomy, depressed shadow of that person.

He couldn't stop grinning every time he came to visit her and saw her almost leap out of her chair in excitement, having been feeling bored to death and knowing that company would also bring an opportunity to do something that she couldn't do on her own. When they agreed that a week seemed like a pretty reasonable observation period, he knew that for Elizabeth, it would mean seven excruciatingly long days with not much to do except read, eat and sleep, which was probably equal to an absolute nightmare for a workaholic like her. For as long as he knew her – and even earlier, given the number of accomplishments at her age – she had never been good at being idle, she had never even been good at taking the rest that she needed, so he wasn't surprised to see her going out of her mind with boredom and looking forward to any visit, no matter how short, even if it was Keller with yet another round of tests.

The doctor was coming by twice a day, looking for any sign of activity from the nanites, which – so far, much to everyone's relief – there had been none. She wasn't Elizabeth's only regular visitor, though; in fact, John made sure that his entire team came to visit her every single day, having established a little pattern of sorts, trying to make it easier for her to go through this week.

Rodney always came in the morning, eating his breakfast with her and sharing his new thoughts and ideas with her, before leaving for his lab to truly begin his day. Much to Elizabeth's surprise, he claimed that his conversations with her helped him improve his ideas. She didn't think she was doing much, especially when she wasn't even sure if she understood what he was talking about, but she figured it could be just the fact that he was putting his thoughts into words that he found helpful and as long as he felt this way, her own opinion didn't really matter.

About an hour after McKay left, it was time for her training session with Ronon. She didn't really expect the Satedan to try to come up with something they could do together, as they didn't really have much in common, so she was quite stunned when he arrived and suggested that he could try teaching her some very basic self-defense moves. She still jumped at the chance, aware that it was something she would most likely have to do anyway sooner or later, if she was to stay in Atlantis and become a member of one of the off-world teams, which was the most likely development if the IOA was to relent. And, much to her surprise, Ronon was turning out to be a pretty good teacher, and quite forgiving as well.

Then, it was John's turn. Out of them all, he was the one that stayed with her the longest, first sharing lunch with her and later moving on to games, as she insisted that between all the reading, training, talking, she needed some entertainment. Over these few days, she accumulated quite a collection – a chess set, two decks of cards and several board game boxes, which John had borrowed from various expedition members – as well as a big box of all kinds of sweets, which John was bringing to serve as currency for their poker games and which she had all won from him.

And, at the end of the day, after her second round of tests, came time for her to hang out with Teyla. Elizabeth wasn't surprised to learn that the training was actually Teyla's idea, but with how overprotective everyone was about her now that she was pregnant, Teyla figured that Elizabeth could be uncomfortable with the idea of her being the one to train with her. Instead, they chose to stick to tea and conversation, sharing all kinds of stories about the history and culture. They might have learnt quite a lot about each other's worlds over the past few years, but they were mostly the things they needed to know in order to successfully cooperate with each other, and these talks made Elizabeth realize just how much. Teyla also began teaching her meditation and even though she wasn't convinced at first, Elizabeth had to admit that it was actually proving to be quite helpful with putting her mind at ease whenever she would begin to overthink everything.

She was still quite surprised when it was Samantha Carter, who showed up just after Keller finished the last round of morning tests on the day when she was supposed to finally leave. She expected John or anyone from his team, maybe even all of them, and she couldn't help feeling a little disappointed as she hoped that once she was out of here, she would get them to tell her more about what she had missed. So far, she had only been getting very general information, just one of the very long list of precautions put in place just in case, and she was very curious about everything.

"Doctor Weir" greeted Sam. "Doctor Keller just confirmed that she sees no reason to keep you here any longer."

"That's great" replied Elizabeth, giving the woman a small, polite smile.

She knew that she should probably be feeling – and showing – more excitement than she actually was, but she found it a little difficult with the little voice in the back of her head telling her that they would never have full certainty that it was safe for her to go back to normal life. As it was, however, she couldn't help feeling a little worried; a feeling that she was trying to ignore in her attempt to stick to the promise she gave John, convincing herself to trust her friends. Still, while she wasn't as excited as one would expect her to be, she was most definitely relieved not to be stuck in this room anymore.

"I know John was hoping you'd eat breakfast with his team, but I'd actually like to steal you, if you don't mind?" suggested Carter and Elizabeth immediately thought how it explained everything.

"Okay, sure" she said, unable to hide her curiosity. The two of them weren't close, so she had no doubts that there must have been a reason behind the Colonel's actions. One that she would probably only find out once they left this place.

They were soon on their way to the cafeteria and, thanks to all the people that they met on their way, the walk took them three times as much time as it normally would. Elizabeth could hardly stop smiling as she kept on bumping into familiar people, all of whom were asking her how she was doing or telling her it was good to see her out an about. It meant a lot to her, and she was glad to see that Carter understood, or at least didn't seem to mind the constant stops.

For Sam, it was pretty much a confirmation that she was right about the sympathy and loyalty that the people in Atlantis felt towards Elizabeth. Being able to see their reaction to the fact that Elizabeth was released from isolation was part of the reason why she wanted to be the one keeping her company during those first moment of regained freedom. This was exactly what she was expecting and even though she could hardly contain a chuckle every time they were approached by yet another person, she would never take it away either from Elizabeth or from these people.

She was glad that they arrived relatively late, after most of the people had already eaten their breakfast and went to their respective posts. Otherwise, she didn't think that even an intervention from Ronon, giving a not too subtle hint that Elizabeth would probably like to eat her meal in peace, would be enough to coerce them into leaving them alone for some time. Now, at least, they were only staring at the two of them curiously, John and Rodney in particular, which made them deliberately choose the table on the other side of the cafeteria to avoid them trying to overhear.

"It's a proof of the amazing job you've been doing here" said Sam, when they finally sat down. "Don't get me wrong, I never claimed that you weren't, but I only fully realized it when I got here, and not as a visit but…"

"When you replaced me" interjected Elizabeth, seeing the other woman struggle, trying to find a way around stating it so bluntly. "It's fine, really. It was to be expected and John speaks quite highly of you, there's no reason to be awkward about it."

"Great, I'm relieved" admitted Sam, smiling slightly. "I'd hate for things to be awkward between us, especially if we are to work together."

"I think we both know that the IOA is not going to be too keen on that" Elizabeth pointed out, tilting her head to the side as an unconvinced expression made its way onto her face. "In a way, I'm surprised that they haven't come to Atlantis with guns blazing yet just because you revived me. Is there any reason why nobody mentioned them to me the entire week, or it was only because of the cameras in the room?"

"Only the cameras" assured Sam. "Most, if not all, of the people here are on your side but we agreed it would be safer if there was no recording of anyone saying that quite so openly."

"Right, better for everyone not to give them any more evidence against themselves. So, what's the news on that front?"

"They're not too happy, as was to be expected" sighed Sam. "They've actually summoned the two of us to Earth."

"They want me to go to Earth?" asked Elizabeth, her eyes widening in surprise.

It was a turn of events that she wasn't expecting. She figured that sooner or later, they would want to question Carter about her permission to enact John and Rodney's plan, but she actually expected them to send a representative, or a delegation, to Atlantis. If they considered her a security risk – and she had little doubts that they did – it didn't really make sense for them to summon her back to Earth, and risk revealing the planet's location to the replicators.

"According to General O'Neill, they realize that they won't be able to even get anywhere near you if they don't separate you from the people in Atlantis. They're probably right about that. I don't see John letting them anywhere near you, and I'm sure his team would help. Actually, I'm pretty sure he won't be too happy about letting you go, either."

"No, he won't" agreed Elizabeth, glancing in the direction of the table occupied by John and his team. The Colonel in question wasn't even trying to be subtle about watching the two of them, and when she caught his gaze, she could easily read the silent question reflected in his features – _everything okay?_ – to which she just gave a tiny nod. "You're hoping I'll convince him not to make a scene, aren't you? That's why you wanted to catch me before he finds out" she asked as her eyes returned to Sam, and the guilty expression on the blonde woman's face was enough to serve as an answer on its own.

"I'm not sure what the IOA wants from you exactly and he's bound to jump to conclusions" said Sam. "You're the only person he'll listen to."

Elizabeth nodded, aware that Sam was right. The moment John would find out about this development, all hell would break loose and she couldn't blame Carter for wanting to avoid it. At the same time, without any specific information, she couldn't exactly blame John for his likely reaction, either. Elizabeth herself wasn't sure what to think about it and her mind was coming up with all kind of ways in which it could go wrong.

She knew that she was being ridiculous and the IOA weren't nearly as bad as her mind was making them up to be. No matter what kind of ideas for what to do with her they would come up with, they were still bound by certain rules and ethics was definitely one of them. Yet, despite the fact that the rational part of her reasoned that they couldn't cross a certain line, the part of her that was freaking out about the entire situation reminded that it probably wouldn't be too difficult to cover it up if they chose to lock her up and turn her into a test subject or force her into exile on another planet.

Her thoughts must have been reflected quite well in the expression on her face, especially combined with her silence, because the moment their gazes met once again, Sam offered her a small, reassuring smile.

"Atlantis is not the only place, where people are on your side" assured Sam. "I promised John that he could trust me, and I intend to keep that promise but I don't think he's willing to believe me until I manage to get _you_ to trust me. I obviously can't speak for everyone, but I can promise you that if it comes to the worst, you can definitely count on SG-1 and General O'Neill."

"Thank you" spoke Elizabeth, taken slightly by surprise.

She knew, of course, that the woman in front of her held a lot of sway on Earth, having earned a wonderful reputation and authority, but the idea that she was willing to use it in order to help her still seemed a little crazy, even though she was aware that she wasn't doing it entirely for Elizabeth. Even this short conversation allowed her to see that Carter believed Elizabeth to hold a certain power over the people in Atlantis and didn't want to be against them. Yet, no matter the reason, it was the result that mattered and even if the Colonel's motivations were to be completely selfish – and she heard and knew too much about her to believe that – Elizabeth would still be grateful for any help she was willing to offer.

"When are we supposed to leave, then?" she asked after a moment.

"Tomorrow" replied Sam. "They initially wanted us to gate to Earth as soon as you're out of isolation, but I thought you could use at least a little break."

"Can't deny that I could" admitted Elizabeth, chuckling softly. "Okay, I'll be ready, then."

"Great. I'm sure it won't be too bad. Even if, I want you to remain a part of Atlantis' team. I doubt they'll ever consider reinstating you as a leader, but they have no reason not to let you stay as a diplomat and a linguist. If you were willing to, of course."

"I'd love that" smiled Elizabeth. "Thank you, Colonel."

"Just Sam, please" replied Carter, extending her hand. "I know that we've never been close but if we are to work together, hopefully, I'd like the two of us to be friends."

"It does sound like we're facing a common enemy already" joked Elizabeth, shaking the woman's hand. "Elizabeth."

The history between them could be a little complicated, but as they exchanged smiles, both of them had a feeling that it wouldn't stand in their way and it was a start of a pretty promising friendship.


	5. Chapter 5

**A/N:** Thank you for your response to this story, especially the reviews. It's nice to see someone is enjoying this little story :) I planned to publish this on Monday, but since this is a John/Elizabeth story and this chapter is pretty much centered on them, I am kind of too eager to publish it, haha. I hope you're going to enjoy it!

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When she arrived in her quarters some time later, Elizabeth noticed that everything was almost exactly as she left it the last time she was in this room. It was difficult to believe that it had been six months since that day. On one hand, having been unconscious for almost all this time, she felt like almost no time had passed and on the other, with all the changes that had happened in Atlantis, it was difficult to believe that it hadn't been longer.

Had she known back then that her life would take such a turn, she would have done many things differently but – in particular – she would have avoided standing in front of that window during takeoff. Had she been watching from any other spot, she would never have been hit by that beam, she would never have needed her nanites to be reactivated in order to save her and finally, Rodney would never have connected her to the replicators' collective as they would never have even thought to take her with them, if they even went to the replicators homeworld in the first place.

The only thing that was out of order was the box that someone left on her desk, which held all of her personal belongings that she used to keep in her office. She smiled as her eyes drifted over the things inside and she absent-mindedly traced them with her finger. There were the Athosian pot that she received from John as a birthday gift during their first year in Atlantis and the wooden figurine of a cat-like animal that was worshipped on one of their allied planets, which John had given her for her second birthday in Pegasus. Her eyebrows furrowed when she initially failed to see his last gift, the rock of an unusual but natural, deep purple colour, which was supposed to be some kind of a lucky charm and which John had had sculpted in the very fitting shape of a four-leaf clover, but she soon found it nestled on the framed picture of Sedgewick, right next to her father's pocket watch.

The last two object made her think of her mother and she immediately began feeling guilty. She couldn't help wondering what she had been told about the past several months. Given Elizabeth's uncertain situation, the Air Force must have told her _something_ to explain why her daughter couldn't visit or contact her in any way but no matter what kind of reason she was given, it had to be serious enough to cover the possibility that she would actually never hear from her again, and Elizabeth could only imagine how it must have made her mother feel.

The last time she had seen her – truly seen her, not in a replicator-induced dream – was over two years ago, when she had come to Earth after they re-established contact with their home planet, and even that was a pretty short visit, which wasn't fair to her mother. She wished she hadn't kept on coming up with all kinds of excuses not to go to DC during the six weeks she spent in Colorado after the Ancients had forced them to leave Atlantis. She hoped that, if everything went according to plan and she was given permission to return to Atlantis, she would get a chance to visit her, apologize and promise that she would at least try to contact and visit her more regularly.

The sound of the door sliding open brought her back to the present and the thud of vigorous, angry steps made her realize that it was finally time for the conversation that she was not looking forward to have. How they had actually managed to keep the development from John for so long was completely beyond her but he had clearly found out about it now.

"Tell me you are not serious" he demanded as he stormed into her quarters.

He didn't even bother using a chime or making sure that he wasn't intruding. It took her slightly by surprise; he had only been here a handful of times but never just walked in like that, always alarming her of his presence and leaving the choice of letting him in to her. The last time she had seen him like this was when he came to her office, annoyed by Woolsey's inquiries and even though he deflected it back then when she teased him about defending her honour, here he was, once again ready to jump to her defense when she was 'threatened' by the IOA.

It was only when he didn't notice her right away that he stopped in the middle of the room, looking around in surprise as he had been certain he would find her there. He relaxed visibly when she finally moved into his field of vision but the determination in his eyes did not waver; if anything, it actually grew stronger.

"I don't have a choice" she said as she stepped towards him, folding her arms around herself when she stopped in front of him.

"Like hell you don't!" he exclaimed and Elizabeth closed her eyes, taking a deep breath as she reminded herself not to get influenced by his emotions and stay calm.

"It's the only chance for me to have a relatively normal life" she pointed out, her voice a little more insistent. "And I don't only mean life on Earth, but also staying here in whatever capacity Carter will have me."

"I guess" grumbled John, unable to argue with that. He knew that if she was to officially stay in Atlantis, she needed permission from Earth's officials and she could only get it by meeting with them. "I'm going too, then. I have more than enough leave saved up and Lorne can easily handle my responsibilities."

"I'm not the person you have to talk to about that" she reminded him and raised one of her eyebrows, when he made a sound that seemed like something between a growl and an irritated huff.

"Carter said no but I'm sure you could convince her."

"No" Elizabeth replied, her voice leaving no doubts that there was nothing he could say to convince her otherwise. "And I don't even want to hear anything about ignoring her and going anyway."

John muttered something under his breath and she didn't manage to catch it, but the expression on his face made it clear that it was exactly what he was thinking about and, if she read him correctly – and she usually did – he was now stuck in conflict between doing what he was convinced he should do and respecting her.

"I appreciate what you are doing" she assured him. "I really do, but I am not going to have you court-martialled because of something stupid like this."

"Screw the court martial!" he burst out. "Your entire future depends on how everything on Earth, I'd hardly call it stupid."

"John…" she began, but he didn't let her finish.

"I'd just feel better if I was there with you" he admitted, lowering his gaze to the floor.

She knew the look on his face quite well. It was the very same expression, which she had learnt to be a sign that he was feeling a little embarrassed and uncomfortable, revealing his true feelings about something. She could see that there was more on his mind and he looked like he was trying to decide whether he actually wanted to say it, and she wasn't sure if she was supposed to give him time to gather his thoughts or save him by changing the subject or at least lightening the mood.

"I can handle it on my own" she assured him, placing her hand on his shoulder. "Besides, Carter's going with me and she has more power on Earth than anyone gives her credit for."

"I know, it's just… I've almost lost you, _twice_, and I don't want to go through this again" he sighed, stuffing his hands in his pocket.

Elizabeth stared at him for a moment, rendered completely speechless by that simple confession. It wasn't even the message itself that took her so much by surprise, but the raw emotions in his voice, which were also written all over his face. She had seen many sides of John Sheppard, she dared claiming that she had seen most of them, but this was something that she had never seen before. She knew he was willing to go far to help her – too far for her liking, but she still appreciated it – yet, she had no idea that he felt quite so deeply about it.

It stirred emotions and feelings in her that she had long buried deep at the very bottom of her heart. Feelings that she had fought hard to push away, to prevent from developing, because falling for John Sheppard was a very bad idea and it wasn't only because of their working relationship. Yes, it would definitely complicate everything between them and – back when she was the leader of Atlantis – it could potentially undermine her position, especially that some already believed that the two of them were together and she was biased. At the same time, however, she was aware that she would only be setting herself up for a heartache; she had seen the type of women he was into and she was pretty much the exact opposite of them and while she wasn't pathetic enough to begrudge anyone any potential relationship, she still didn't like the idea of being forced to watch it.

She had failed, of course. She had been in denial, believing that she had succeeded, convincing herself that the pressure she felt in the pit of her stomach whenever he, once again, found himself in danger wasn't any different than her worry about Rodney or anyone else in Atlantis. At least until yet another close call happened, and the way she felt before his team returned to Atlantis made it impossible for her to fool herself any longer.

Luckily, she had always been very good at acting professionally in any situation and not revealing how she actually felt, at least until now. Did he even realize how it made her feel, when he was saying something like this with eyes so full of emotions? Not even bothering to use 'we', which would imply that he was speaking about the people in Atlantis, but speaking about his own, personal feelings.

"John" she spoke up, trying to coax him into looking at her again.

She wanted to assure him that it wouldn't happen and even though she didn't think the IOA would go quite so far, she was aware that she couldn't give him any promises that it would be fine. They might not do anything that would endanger her life, but they could create all sorts of other problems and she had a feeling that her being forbidden to return to Atlantis was also one of the situations that John was talking about.

He reacted only when she stepped closer and stood on her toes, wrapping her arms around him in what she hoped would be at least slightly reassuring hug. His arms tightened around her almost immediately, such a far cry from that one time she hugged him after he returned to Atlantis, having been saved by the Daedalus. Instead of awkwardly, he was holding her tightly, almost as if he was trying to send a message that he didn't want to let go.

"I can't lose you, Lizbeth. When Keller said that you'll most likely never wake up, I just…" he paused for a moment, looking for the right words. "_I can't lose you_."

Elizabeth was stunned once again, understanding what he was trying to say even before she pulled away and saw the way he was looking at her. It was only the look in his eyes that truly silenced the little voice in the back of her head that was telling her she misunderstood, that she was reading too much into it. And she knew exactly what he was talking about, how the whole situation made him feel; she had been in his shoes, after all. It had also been a close call that made her realize how much she actually cared about him, when the reality of the possibility of losing him sank in.

At the same time, she wasn't sure if knowing that he felt this way made her feel more relieved or more terrified. She was glad, of course, that it wasn't one-sided as she had previously believed but with how different the two of them were, she wasn't sure they could make it work if they decided that they wanted to give it a try. The idea that it wouldn't work out scared her more than anything because she didn't want to lose John in any way; not only in the sense that something could happen to him but she didn't want to lose him as a friend, either.

That, however, was something to think about when – if – she returned to Atlantis. For now, the priority for her was to make sure that she was allowed to keep her life and everything that came along with it, or figuring out what to do if the authorities on Earth decided that it was too big of a risk.

"It'll be fine" she assured him, taking his hand into hers and giving it a gentle squeeze. "I know that I can't be sure of anything but Carter and General O'Neill have a plan. She promised me that no matter what happens, he'll figure something out and as much as I don't like the idea of relying on others, I don't really have a choice but to trust them."

For a moment, John wanted to argue with her, make her realize that it wasn't her only choice and all she needed was to say a word for him to alert Rodney, pack his things and take the jumper, but he didn't. It was clear that she wanted to avoid it and not only because it would also affect other people; she clearly didn't like the idea of leaving everything behind and even though he didn't really know why, he figured that she had her reasons.

"Fine" he agreed reluctantly. "I still don't like it but we'll do it your way."

"Thank you" she smiled and leaned into him when he pulled her back into a hug.

She could feel her cheeks get warmer when he placed his hand at the back of her head and pulled her closer, pressing his lips against her forehead. It felt almost like a promise that he wouldn't let anything happen to her, and she had no doubts that he meant it. Somehow, she had no doubts that should the worst case scenario happen, he would figure out a way to break her out of anywhere on Earth as well and it was the thought that she had someone like John in her life that made her feel hopeful that it really was going to be okay.


	6. Chapter 6

**A/N:** I'm sorry for the delay with this chapter. I had it all ready, only to realize that I've completely messed up SGA's timeline and ended up rewriting it completely. Anyway, here it is now. I think the next one will probably be a little delayed as well, but then I hope to be back to the schedule I wanted to keep. Thank you for the response to this story and enjoy!

* * *

Even though she was doing her best to stay positive, the closer it came to the time when she and Carter were supposed to leave for Earth, the more difficult it was for Elizabeth not to feel nervous. The night, however, turned out to be the worst; it was quite easy not to think too much about it when she was in the company of her friends, but as soon as they left her on her own to get some rest, her mind went into overdrive.

As a result, she had gotten almost no sleep at all the entire night. Even when she finally managed to fall asleep, she dreamt about being locked up in high-security facility – very similar to the one, which the nanites made her dream about, only it was more of a prison, located on a remote island, an escape from which was pretty much impossible.

In the end, she gave up on sleep and chose to go for a walk around the city instead. As much as she enjoyed seeing it bustling with life, walking down the empty corridors allowed her to take in the beauty and charm of Atlantis that she had come to love in the first place. Within three short years, this city had become the first place in a long time where she felt truly at home, and here she was, once again facing the possibility that once she stepped through the gate in the morning, she might never see it again.

It was actually the reason why she decided to take a walk instead of staying in her quarters. Now, that most of the people were asleep, she could walk around peacefully, instead of being stopped at every corner by those, who wanted to let her know that it was good to see her again. She appreciated the words but they still made it difficult to take a simple walk. She couldn't do that when she was with John and the rest of his team, either; the main reason she wanted to take it was to commit the place to her memory in the case she ended up not returning, and all of them would protest, insisting that she shouldn't be thinking that way.

She wasn't sure how long she was walking around, visiting all of the familiar spots, fondly remembering everything that happened there. It was only when she noticed the sky starting to brighten as she stood on the control room balcony that she was brought back to the present, realizing that it wasn't going to be long before Atlantis wakes up and only a little longer before she was scheduled to leave.

That time, in fact, came much faster than she wished and before she knew it, she found herself standing in front of the gate with a bag full of her belongings – mainly clothes, but she also decided to take her father's watch and the supposedly lucky purple rock. Feeling someone's eyes on her, she looked up and noticed John, standing by the railing on the upper level of the gate room. With his jaw clenched and arms crossed on his chest, he wasn't even trying to hide that he still wasn't happy about her leaving and him staying behind, but she was glad to see that he wasn't going to go back on his word.

"Are you ready?" asked Sam, walking down the stairs of the control room when Chuck began to dial the gate.

"As ready as I'll ever be, I guess" she replied, trying to sound more confident than she felt when the gate opened with a swoosh, the blue event horizon managing to look more uninviting even than that one time she had gone to the Genii to convince them to share their nukes with Atlantis.

"Let's go, then" spoke Sam, offering a reassuring smile before she walked through.

Elizabeth moved to follow but stopped in the last moment, turning around to take one last look around the room. Her eyes lingered for a moment on John and she didn't miss the way he looked at her, almost as if trying to say that she only needed to say a word for him and McKay to take over Atlantis or get a jumper. Instead, she just raised her hand in a farewell gesture, smiling when she was reminded of how John did the exact same thing that first time they used the gate in Atlantis when it was her standing in that very same spot where he was now. Letting out a heavy sigh, she finally turned around and stepped through the gate, unaware of the fact that Rodney stopped at John's side at almost the same time as she disappeared.

"Are you sure it's a good idea?" he asked, looking even more uncomfortable than his friend when the gate shut down.

John's annoyed grumble was the entire answer he needed to have no doubts that he wasn't the only one, who couldn't help coming up with more and more ideas of what could go wrong. He might have done everything he could to give Elizbaeth a chance to live normally despite the nanites, making sure that they would remain harmless for the rest of her life, but he had no way to prove that what he had done was foolproof. He couldn't even be _entirely_ sure himself, no matter how confident he was about his work. There would always be a chance that the nanites would find a way around it, even if it was an extremely tiny one and with the IOA in mind, even that seemed too big.

"Why did you let her go, then?"

"It's the only way for things to get back to normal for her" replied John and snorted, when he realized that he just repeated the argument Elizabeth had used on him.

"Do you really think the IOA are going to let it happen?"

"No" admitted Sheppard. "But Carter and O'Neill may find a way to leave them no choice."

"So we're just going to sit back and wait?" asked Rodney, disbelief clear in his voice.

He had no idea what Elizabeth had said to him, but he didn't think that there was anything she could say to make him give up on helping her. Unless she told him that she didn't want to stay in Atlantis but he couldn't imagine something like that. She loved this place, after all, she was willing to die for it and he remembered quite clearly what she was like during the six weeks after the Ancients had returned – there was no way this could be the case. Sheppard, of course, didn't disappoint him in the slightest.

"_We_" the Colonel began, finally turning to look at his friend, "are going to come up with a plan to break Elizabeth out of anywhere that they may keep her prisoner on Earth."

"Now you're talking" spoke Rodney but the grin that initially appeared on his face slowly faded away as he realized that there was a tiny issue with John's idea. "You do realize they may actually take her someplace other than Earth, so that nobody is able to stop whatever evil plan they might have for her, right?"

John looked at him incredulously. He thought that he was the paranoid one, coming up with potential scenarios that even he didn't find too believable himself yet, clearly, he really shouldn't underestimate Rodney when it came to something like that.

"Right. We'll think of a way to figure out where they took her too" he said. It was better to be prepared for everything, after all.

* * *

At the same time, Elizabeth materialized in the Midway Station. She didn't even realize until that very moment that it was the first time she was there after it was finished, and she couldn't help feeling a little disappointed by what it looked like, especially compared to the aesthetics of Atlantis. It wasn't built to win a prize for the best interior design, though, but to serve a certain function and that she knew it did.

"Colonel Carter, Doctor Weir" spoke one of the technicians assigned to the station, who went out to greet them. "Welcome to the Midway Station. If you follow me, I'll show you to your quarters."

"Quarters?" asked Elizabeth, looking at Sam in surprise when the blonde woman just nodded.

"Right, I'm sorry. I keep forgetting you don't know about anything that happened over the past few months" said Sam as they began walking through the station. "We have to go through a twenty-four hour quarantine period. It's one of the safety precautions put in place after Kirsan fever broke out in Atlantis" she explained.

"I see" murmured Elizabeth and Sam smiled, when she realized that the other woman didn't find the explanation too useful.

"Kirsan fever is a common Pegasus disease. It's not unlike many diseases on Earth, in the sense that you go through it once in your life and later build up immunity, so most of the time it's children that come down with it. Only we don't have it on Earth, so when it was brought to Atlantis, it was just a matter of time before everyone except for Ronon and Teyla was affected."

"And the quarantine is there to make sure that we don't end up bringing it to Earth" Elizabeth nodded, knowing it made sense. The last thing anyone needed was for them to infect people on Earth with something native to another galaxy.

"Exactly" confirmed Sam, smiling to the technician when he indicated the room where the two of them were supposed to stay in before he walked away. "Top or bottom?" she asked, motioning towards the bunk bed in the tiny room.

"Bottom" answered Elizabeth, sitting down and looking around.

She smiled, when she noticed a small collection of books, movies and games that was undoubtedly put there to make the quarantine period at least a little easier. Sam immediately moved to get a closer look and turned around with a grin, showing her a deck of cards.

"Looks like I'll finally have a chance to see those incredible poker skills that Daniel has told me about."

Yet, even despite those objects, twenty four hours later both of them were more than ready to leave. Elizabeth couldn't help feeling a little underdressed when she noticed that Sam had actually put on her dress blues, but quickly shrugged it off. She figured that she would probably be taken for some tests to confirm the results of those conducted in Atlantis, so it wasn't going to make much of a difference. And she wasn't mistaken.

She was ushered to the Stargate Command's infirmary as soon as they exchanged greetings with Generals O'Neill and Landry. What took her by surprise, however, was the less than pleased expression on Doctor Lam's face when she arrived. As it turned out, the doctor wasn't too happy with redoing all the tests that had already been performed, seeing it as a waste of time, and only agreed because General O'Neill had asked. It was, apparently, a compromise between accepting the results from Atlantis and having her examined by an independent expert chosen by the IOA.

"Sorry for all that" stated Jack O'Neill, when he came into the infirmary after all of the tests were finished. "It was the only way to convince everyone that Atlantis' results are accurate."

"What now, then?" she asked, trying her best to reflect it in her voice that she understood and wasn't going to resist going along with whatever was necessary. "Isolation room until the results are in?"

"Actually, I managed to get you out of that one" he said, puffing out his chest in pride playfully before he smiled. "You can walk freely around the base, but you have to be accompanied by a guard with an ARG at all times."

The guard turned out to be Teal'c, recommended for the job personally by O'Neill as a part of the General's plan to make sure that the IOA wouldn't get any opportunity to even try to make any potential attempt at going too far. He kept on saying that it was because he had promised Carter to make sure that everything would go smoothly and he didn't want to take any chances, but Elizabeth couldn't shake off a feeling that there was something he wasn't telling her, almost as if he knew something that he didn't want her to know or worry about.

_Or you're just being paranoid_ – she told herself as she walked to the commissary with Teal'c walking silently behind her. She suddenly had a very good idea what it must have felt for everyone, whom she ordered Ronon to have an eye on so many times in Atlantis, but she was actually quite happy with the choice, knowing that his loyalty was first and foremost with his friends from SG-1, which included O'Neill and Carter, so he was someone that she could trust, even if she couldn't count on much of a conversation. She did, however, suspect that he was a very good listener and she had a feeling that with the IOA interviews looming over her in the near future, she would be using that particular 'skill' of his quite a lot.


End file.
